Any small air leak in the path to the sea water pump, will cause issues since anything upstream from the pump is undergoing suction.
Likely suspects:
Water neck fitting and special beaded gasket
S hose connection at same.
Lower pivot tube Oring
Suction hose breach
Scored or bad thrust surface and/or cam within the pump body
New impeller of incorrect type/size for the pump body (you do not list which engine or pump).
There are some issues with a Johnson and Jabsco impeller that looksidentical to one another, but are not.
This would be for a crankshaft style pump.